SMTL ID : 8pvf.1

Structure of GAPDH determined by cryoEM at 100 keV

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 23 residues within 4Å: Chain A: N.23, G.24, F.25, G.26, R.27, I.28, N.48, D.49, P.50, F.51, M.52, A.93, K.94, S.112, T.113, G.114, F.116, S.136, A.137, C.168, A.199, N.334, Y.338 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.28, A:I.28, A:Y.338 Hydrogen bonds: A:F.25, A:R.27, A:I.28, A:N.48, A:K.94, A:N.334 pi-Stacking: A:F.51 NAD.2: 23 residues within 4Å: Chain B: N.23, G.24, F.25, G.26, R.27, I.28, N.48, D.49, P.50, F.51, M.52, A.93, K.94, S.112, T.113, G.114, F.116, S.136, A.137, C.168, A.199, N.334, Y.338 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.28, B:I.28, B:Y.338 Hydrogen bonds: B:F.25, B:R.27, B:I.28, B:N.48, B:K.94, B:N.334 pi-Stacking: B:F.51 NAD.3: 23 residues within 4Å: Chain C: N.23, G.24, F.25, G.26, R.27, I.28, N.48, D.49, P.50, F.51, M.52, A.93, K.94, S.112, T.113, G.114, F.116, S.136, A.137, C.168, A.199, N.334, Y.338 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.28, C:I.28, C:Y.338 Hydrogen bonds: C:F.25, C:R.27, C:I.28, C:N.48, C:K.94, C:N.334 pi-Stacking: C:F.51 NAD.4: 23 residues within 4Å: Chain D: N.23, G.24, F.25, G.26, R.27, I.28, N.48, D.49, P.50, F.51, M.52, A.93, K.94, S.112, T.113, G.114, F.116, S.136, A.137, C.168, A.199, N.334, Y.338 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.28, D:I.28, D:Y.338 Hydrogen bonds: D:F.25, D:R.27, D:I.28, D:N.48, D:K.94, D:N.334 pi-Stacking: D:F.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McMullan, G. et al., Structure determination by cryoEM at 100 keV. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-11-29

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glyceraldehyde-3-phosphate dehydrogenase

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